Well I'm going to stick with 3D on this just because there's so so much 2D out there on DS and quality is more of an opinion at that level.
Now as far as 3D goes I can list a few 'currently out in the NA region' that get a big nod.
Call of Duty 4: Insane 3D engine, smooth FPS too, very high detail and large structures, and all done in 3D right down to some very impressive destructible walls and fiery explosions. Everything in this game while a more bland color set due to the region it plays in has a very high level of detail I hadn't seen before on the DS. Even the stages in motion (on a blackhawk, high up night vision in a c130, or in a hummer) are very detailed and keep smooth swishing around the stages never missing a beat.
Final Fantasy CC - RoF: Much like COD4 this again has a very rich 3D engine and also has a steady framerate. This game took that original engine that FF3 used and learned a few new tricks in smoother visuals, more colorization, less pixelization (little squares on polys being so obvious), and all the characters, spells, and attacks are quite fluid and varied. Also a nod needs to go to DQM: Joker because it too uses this same engine, but goes with a toon cell shaded style here, so while looking less detailed still does wonders.
Brothers in Arms/Assassins Creed: I 'slashed' that as they use the same 3D engine Gameloft created which is mostly sound. While these two games I could say perhaps have a bit more detail on the polygons than others in the list in some places the trade-off is that you get some pop-through on some polygons(clipping) and some bad slowdown when things get hectic. The slowdown won't get you killed but you'll feel it and have to adjust slightly. That said though both the games are fun, though BiA is more replayable due to design than the other that's a one play wonder.
...I saw FF4 DS listed already by a person or two and so far what we've had shared to us it does trump these games, so it obviously shows there's great room still yet for improvements as engines are tweaked, but it stayed off the list as it's not out yet beyond Japan making it unplayable for most.
And yes I left Metroid off this list as while visually it was pretty decent, it was also quite bland and didn't vary much, and detail wise its lesser than what I listed but that's to be expected as it was a first.
